Variant report

Variant	rs177254
Chromosome Location	chr12:29733790-29733791
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10400534	1.00[CEU][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10400541	1.00[CEU][hapmap];0.83[JPT][hapmap];0.95[EUR][1000 genomes]
rs10492312	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10771550	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10771551	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10771552	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10771553	0.81[JPT][hapmap]
rs10843445	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11050284	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11050285	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11050308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12372765	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs1326758	1.00[CEU][hapmap];0.83[JPT][hapmap];0.97[EUR][1000 genomes]
rs1409615	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs148898	0.96[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1529908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs159685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs159687	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159690	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159694	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs159695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159696	0.83[JPT][hapmap];0.97[EUR][1000 genomes]
rs159697	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159699	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs159700	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs159702	0.89[YRI][hapmap]
rs159713	0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap]
rs159716	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs1863224	0.95[JPT][hapmap]
rs2081429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2113879	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs2113880	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs2162033	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2194819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2209660	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs2209661	0.95[JPT][hapmap]
rs2209662	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs2225065	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs2243623	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2254945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2288131	0.86[CEU][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs2288230	0.91[ASN][1000 genomes]
rs2350532	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs2710775	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2766599	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2766600	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2766601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2766602	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2766604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299444	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs299445	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs299453	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs299454	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs299456	0.87[EUR][1000 genomes]
rs299457	0.87[EUR][1000 genomes]
rs299458	0.81[ASN][1000 genomes]
rs299462	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs299463	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs299464	0.89[ASN][1000 genomes]
rs299465	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs299466	0.96[CHB][hapmap];0.89[ASN][1000 genomes]
rs299467	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299468	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299469	0.88[AMR][1000 genomes]
rs299470	0.95[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299471	0.86[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299472	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs299475	0.95[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs299479	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs299487	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs366998	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3910440	0.83[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs3910441	0.82[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs4931204	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57231427	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7311193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7959535	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs7960782	0.95[JPT][hapmap]
rs7965227	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs994171	0.87[CHB][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv469190	chr12:29612425-29811471	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv557917	chr12:29612425-29811471	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1053629	chr12:29680163-29826626	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv529328	chr12:29692414-30246209	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29700400-29734000	Weak transcription	Brain Anterior Caudate	brain
2	chr12:29709800-29756200	Weak transcription	HMEC	breast
3	chr12:29712600-29734600	Weak transcription	Liver	Liver
4	chr12:29713200-29742600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:29716200-29764800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:29717600-29734800	Weak transcription	NHLF	lung
7	chr12:29717600-29736400	Weak transcription	Psoas Muscle	Psoas
8	chr12:29720200-29735000	Weak transcription	NHDF-Ad	bronchial
9	chr12:29720200-29735800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr12:29720200-29743600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr12:29722400-29735400	Weak transcription	HSMMtube	muscle
12	chr12:29722600-29735200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr12:29722600-29736400	Weak transcription	Fetal Stomach	stomach
14	chr12:29722800-29735400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:29722800-29735800	Weak transcription	Fetal Kidney	kidney
16	chr12:29723000-29735200	Weak transcription	HSMM	muscle
17	chr12:29725600-29735600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr12:29725800-29735200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:29726000-29751400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:29726200-29734600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr12:29726200-29735200	Weak transcription	Aorta	Aorta
22	chr12:29727000-29735200	Weak transcription	Fetal Muscle Leg	muscle
23	chr12:29727000-29735200	Weak transcription	Right Atrium	heart
24	chr12:29727200-29733800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:29727800-29735400	Weak transcription	Fetal Heart	heart
26	chr12:29728800-29735200	Weak transcription	Spleen	Spleen
27	chr12:29729000-29734000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr12:29729400-29744000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:29730400-29736200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:29730600-29735600	Weak transcription	Right Ventricle	heart
31	chr12:29731000-29735200	Weak transcription	Brain Hippocampus Middle	brain
32	chr12:29731000-29742600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:29731400-29735600	Weak transcription	Small Intestine	intestine
34	chr12:29731800-29733800	Weak transcription	Adipose Nuclei	Adipose
35	chr12:29731800-29733800	Weak transcription	HUVEC	blood vessel
36	chr12:29731800-29733800	Weak transcription	Osteobl	bone
37	chr12:29731800-29734400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:29731800-29769600	Weak transcription	Hela-S3	cervix
39	chr12:29732000-29733800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:29732000-29737200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr12:29732200-29735400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr12:29732200-29737200	Enhancers	Colon Smooth Muscle	Colon
43	chr12:29732400-29735200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:29732600-29733800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr12:29732600-29734600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr12:29733000-29734200	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr12:29733000-29734400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:29733400-29733800	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr12:29733400-29735200	Weak transcription	Left Ventricle	heart
50	chr12:29733600-29734000	Strong transcription	Muscle Satellite Cultured Cells	--

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